Long circulating RNAs identified as biomarker candidates for risk stratification in childhood acute lymphoblastic leukemia

Analysis of tumoral RNA is essential for childhood acute lymphoblastic leukemia (ALL) diagnosis and prognosis to detect mutations, cryptic fusions and gene expression patterns. Small vesicles circulating in the blood, such as exosomes carry nucleic acids that might be involved in cancer formation and progression, thus presenting a potential for discovery of non-invasive biomarker for diagnosis and monitoring. Here we report the identification of 47 circulating exosome-encapsulated RNA transcripts (30 mRNAs, 5 lncRNAs, 9 circRNAs and 3 pseudogenes) constituting putative biomarker in 2 molecular subgroups of childhood ALL patients. Exosomes were purified from peripheral blood collected at diagnosis from 10 patients positive for the ETV6-RUNX1 and TCF3-PBX1 fusions as well as from conditioned culture medium (CCM) of their representative cell models. Long transcriptome profiling via total RNA sequencing, supported by the implementation of a novel data analysis pipeline confirmed the presence of mRNAs, fusion transcripts, long non-coding and circular RNAs in exosomes. Differential expression analysis comparing tumoral and exosomal RNA revealed 2 transcripts enriched in both leukemic subtypes while 38 were exclusively enriched in ETV6-RUNX1+ patients and 7 were exclusively enriched in TCF3-PBX1+ patients. These are the first results highlighting specific enrichment of long RNA transcripts in exosomes among two distinct ALL subtypes, suggesting the need for investigation of larger cohorts to identify and validate novel circulating biomarkers.